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Team:USTC Software/Standard
From 2009.igem.org
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In wet lab experiment, kinetic parameters are notorious for their difficulties to be obtained quantitatively. To construct a well fabricated device, the kinetic parameters are crucial for an extensible part. When certain parts are placed in the network, certain biochemical reactions with holding kinetic parameters are introduced. To identify kinetic parameters of basic devices determines the extensibility of devices. | In wet lab experiment, kinetic parameters are notorious for their difficulties to be obtained quantitatively. To construct a well fabricated device, the kinetic parameters are crucial for an extensible part. When certain parts are placed in the network, certain biochemical reactions with holding kinetic parameters are introduced. To identify kinetic parameters of basic devices determines the extensibility of devices. | ||
| - | + | <br /> | |
| - | [https://2009.igem.org/Team:USTC/Modeling/Model-2 Model 2]<partinfo>K176126 DeepComponents</partinfo> is a subsystem of [https://2009.igem.org/Team:USTC/Modeling/Model-3 Model 3]<partinfo>K176066 DeepComponents</partinfo>. | + | <br/> |
| + | [https://2009.igem.org/Team:USTC/Modeling/Model-2 <font size = "4">Model 2</font>]<partinfo>K176126 DeepComponents</partinfo> <br/>is a subsystem of <br/>[https://2009.igem.org/Team:USTC/Modeling/Model-3 <font size = "4">Model 3</font>]<partinfo>K176066 DeepComponents</partinfo>. | ||
[[Image:wet2dry.png|center|500px|thumb|[https://2009.igem.org/Team:USTC/Modeling/Model-2 Model 2] and [https://2009.igem.org/Team:USTC/Modeling/Model-3 Model 3] from [https://2009.igem.org/Team:USTC/Modeling 2009 USTC Wet Team]]] | [[Image:wet2dry.png|center|500px|thumb|[https://2009.igem.org/Team:USTC/Modeling/Model-2 Model 2] and [https://2009.igem.org/Team:USTC/Modeling/Model-3 Model 3] from [https://2009.igem.org/Team:USTC/Modeling 2009 USTC Wet Team]]] | ||
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Here we put forward another feasible way to define dynamic parameters of biochemical reactions, and further characterization of single biobrick and combined bio-devices, in terms of chemical dynamics view. | Here we put forward another feasible way to define dynamic parameters of biochemical reactions, and further characterization of single biobrick and combined bio-devices, in terms of chemical dynamics view. | ||
| - | Data Sheet and Related Construction. | + | *Data Sheet and Related Construction. |
| - | # A pool of standard reactions should be constructed according to following suggested rules. | + | *# A pool of standard reactions should be constructed according to following suggested rules. |
| - | ## Clear characterazation of reacting substances, grouped by reactants and products. | + | *## Clear characterazation of reacting substances, grouped by reactants and products. |
| - | ### | + | *### (required)reactants' serial number, names and number of types |
| - | ## Finite division of reaction types, | + | *### (required)products' serial number and names and number of types |
| + | *## Finite division of reaction types (with unique serial numbers for each). | ||
| + | *### (required)Reaction type (used for mathematical modeling, including Hill, Linear, etc.) | ||
| + | *### (required)Parameters' names, values and number of types according to selected reaction type | ||
| + | *### (optinal, default to be independent)Temperature dependence of parameters listed above, each described by an analytical function or quasi-continuous experimental data in deriative form | ||
| + | *### (optional)Other requirements, including reaction compartment, external magneitc field, lighting condition, etc. | ||
| - | # A pool of standard substances (applicable to any unit depictable by reaction types listed in the pool of reactions, including BioBricks, BioDevices, individual cell or even colony) | + | *# A pool of standard substances (applicable to any unit depictable by reaction types listed in the pool of reactions, including BioBricks, BioDevices, individual cell or even colony) |
| - | ## (required) substance's serial number and name. | + | *## (required) substance's serial number and name. |
| - | ## (optional) substance's general physical properties, including molecular mass, magnetism, phase diagram, infrared spectra, etc. | + | *## (optional) substance's general physical properties, including molecular mass, magnetism, phase diagram, infrared spectra, etc. |
| - | ## (optional) substance's general chemical properties, including chemical composition, hydrolysis constant, ionization constant, and the stability in conventional intermediate like air and distilled water, etc. | + | *## (optional) substance's general chemical properties, including chemical composition, hydrolysis constant, ionization constant, and the stability in conventional intermediate like air and distilled water, etc. |
| - | ## '''(crucial)''' type (small molecule, DNA, mRNA, etc.), related reaction | + | *## '''(crucial)''' type (small molecule, DNA, mRNA, etc.), related reaction |
Revision as of 16:28, 21 October 2009
Kinetic Parameters Identification
First of all, we shall clarify that, being dedicated to dry lab experiments, we naturally doesn't have as many incarnated Bio-Parts as usual wet labs do.
In wet lab experiment, kinetic parameters are notorious for their difficulties to be obtained quantitatively. To construct a well fabricated device, the kinetic parameters are crucial for an extensible part. When certain parts are placed in the network, certain biochemical reactions with holding kinetic parameters are introduced. To identify kinetic parameters of basic devices determines the extensibility of devices.
Model 2
is a subsystem of
Model 3.
Here we put forward another feasible way to define dynamic parameters of biochemical reactions, and further characterization of single biobrick and combined bio-devices, in terms of chemical dynamics view.
- Data Sheet and Related Construction.
- A pool of standard reactions should be constructed according to following suggested rules.
- Clear characterazation of reacting substances, grouped by reactants and products.
- (required)reactants' serial number, names and number of types
- (required)products' serial number and names and number of types
- Finite division of reaction types (with unique serial numbers for each).
- (required)Reaction type (used for mathematical modeling, including Hill, Linear, etc.)
- (required)Parameters' names, values and number of types according to selected reaction type
- (optinal, default to be independent)Temperature dependence of parameters listed above, each described by an analytical function or quasi-continuous experimental data in deriative form
- (optional)Other requirements, including reaction compartment, external magneitc field, lighting condition, etc.
- Clear characterazation of reacting substances, grouped by reactants and products.
- A pool of standard reactions should be constructed according to following suggested rules.
- A pool of standard substances (applicable to any unit depictable by reaction types listed in the pool of reactions, including BioBricks, BioDevices, individual cell or even colony)
- (required) substance's serial number and name.
- (optional) substance's general physical properties, including molecular mass, magnetism, phase diagram, infrared spectra, etc.
- (optional) substance's general chemical properties, including chemical composition, hydrolysis constant, ionization constant, and the stability in conventional intermediate like air and distilled water, etc.
- (crucial) type (small molecule, DNA, mRNA, etc.), related reaction
- A pool of standard substances (applicable to any unit depictable by reaction types listed in the pool of reactions, including BioBricks, BioDevices, individual cell or even colony)
